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Southern beekeepers are starting to close their hives down for winter after patchy harvests of honey and the worst summer some can remember in decades.

"It is one of the worst seasons I've ever had in about 30 years," John Stevenson, of Southern Lakes Honey in the Te Anau basin, said.

He said January was "a complete write-off" because it was just too cold for bees to work his apiaries' main crop of clover.

"You need temperatures above 20 degrees and you could count the number of days [in January] above 20 degrees on one hand."

His hives collected a little honey in early December but the bees consumed most of that during a cool January. "The season is really all over," Mr Stevenson said. "The honey is still trickling in and I think we'll end up with about half a crop."

He said he had heard southern beekeepers had harvested a bit of manuka and kamahi bush honey, but the manuka honey crop was "patchy" and well down at about an eighth the size of a normal harvest.

In Otago, beekeepers confirm a similar pattern of patchy, inconsistent harvests.

"To get a good honey crop, you need the heat and flowers when the bees are strongest, which is mid-summer, and we haven't really had a summer," president of the Otago branch of the National Beekeepers' Association Peter Sales said.

"My experience so far this year is very inconsistent harvests. In a poor year results are very patchy between favourable sites and less favourable ones."

"It's still a bit early to tell and sometimes things turn out better than you thought they would but you haven't got the honey until it's in the drum."

Mr Sales said the season started well but strong hives ended up consuming their honey reserves during cold, cloudy and windy periods.

Parts of the Maniototo that had warmer temperatures had a pretty good season and thyme honey harvests in Central Otago had been good with reports of 25 to 30 kilograms of honey from each hive.

Some beekeepers in the Catlins had reasonable crops of kamahi honey but Mr Sales said clover crops throughout the region had been very patchy.

"I've also heard clover root weevil has been quite significant and a lot of farms just don't seem to have the clover on them this year."

He said beekeepers were now "walking a tightrope" to harvest the last of their honey crop before treating hives for varroa and closing them down for winter.

The hot and cold extremes of weather have had an impact on Central Otago honey crops, says Peter Ward, of Alpine Honey in Hawea.